feat: update research skills part 1

[sixiang-svg]

New Skill Contribution

Skill Info

• Skill ID:
• Category:
• Description:

Checklist

• SKILL.md has valid YAML frontmatter with all required fields
• Skill ID matches the directory name
• Category is one of: productivity, development, communication, writing, research, other
• Instructions are clear and self-contained
• Instructions are under 4000 tokens
• No external URLs referenced in instructions
• Tested the skill with an AI agent and it produces good results
• Added usage examples in the frontmatter

Testing

Describe how you tested this skill:

Notes

Any additional context or notes for reviewers.

[markusha77]

Resolve the failed check

[sixiang-svg]

Duplicate resolved, please review them. I am sorry for not being proactive enough before. Please let me know what I can do to help with connectors or other things via slack or emails, I will catch up.

…

On Tue, 17 Mar 2026 at 10:53, markusha77 ***@***.***> wrote: *markusha77* left a comment (ChatAndBuild/chatchat-skills#52) <#52 (comment)> Resolve the failed check — Reply to this email directly, view it on GitHub <#52 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/B63L54XYZHVRA6RSDHGNSND4RC42XAVCNFSM6AAAAACWTQNJDGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DANZRHE4DIOBVG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[greptile-apps]

Greptile Summary

This PR performs a batch normalization of 20 Research skill SKILL.md files, standardizing their YAML frontmatter (adding requires: [], examples, consistent field ordering, and flattening nested metadata: fields) and replacing verbose, code-heavy instruction bodies with cleaner natural-language behavioral instructions. While the frontmatter normalization and instruction rewrites are generally well-structured, several systematic issues need to be resolved before merge:

• ## ## double-hash header bug: Five files (biorxiv-database, brenda-database, bioservices, box-least-squares, camb-cosmology-calculator) have all of their body section headers written as ## ## Instruction, ## ## When to Use, and ## ## Output, which produces malformed Markdown headings that will render incorrectly.
• Inconsistent category casing: Four files (agent-pagerank-analyzer, arboreto, astronomy, astropy) use category: research (lowercase) instead of the repository-standard category: Research (title case), which may break category-based routing or filtering.
• External URLs in skill bodies: Three files (biopython, audit-support, ab-test-setup) retain external URLs in their instruction bodies, violating the contribution checklist requirement that skills be self-contained with no external URL references.
• Missing trailing newlines: Seven files are missing a final newline character, which is a POSIX text file standard violation.
• PR description checklist is empty: None of the contribution checklist items have been checked, and the Skill ID, Category, and Description fields in the PR template are all blank.

Confidence Score: 2/5

• Not safe to merge as-is — five files have malformed Markdown headings, four have category casing inconsistencies, and three retain external URLs violating the contribution guidelines.
• The PR introduces no runtime-breaking code changes (these are Markdown instruction files), but it does contain a widespread and systematic Markdown formatting bug (double ## headers in 5 files) that will cause the affected skills to render incorrectly for end users. Additionally, the category casing inconsistency could break category-based filtering depending on how the platform processes these values. These issues affect roughly half the files in the PR and should be straightforward to fix.
• All five files with the double-hash header bug require immediate attention: skills/Research/biorxiv-database/SKILL.md, skills/Research/brenda-database/SKILL.md, skills/Research/bioservices/SKILL.md, skills/Research/box-least-squares/SKILL.md, and skills/Research/camb-cosmology-calculator/SKILL.md.

Important Files Changed

Filename	Overview
skills/Research/biorxiv-database/SKILL.md	Frontmatter updated with examples and requires; but body sections use ## ## double-hash headers (## ## Instruction, ## ## When to Use, ## ## Output) that will render incorrectly.
skills/Research/brenda-database/SKILL.md	New YAML frontmatter with examples is clean, but body contains the same ## ## double-header bug seen in biorxiv-database, bioservices, box-least-squares, and camb-cosmology-calculator.
skills/Research/bioservices/SKILL.md	Frontmatter updated correctly; body uses ## ## double-prefix on all three section headers, causing malformed Markdown headings.
skills/Research/box-least-squares/SKILL.md	Frontmatter restructured cleanly; all three body section headers (## ## Instruction, ## ## When to Use, ## ## Output) have the double-hash formatting bug.
skills/Research/camb-cosmology-calculator/SKILL.md	Cosmology calculator skill reformatted; suffers from the same ## ## double-hash header bug and a missing trailing newline.
skills/Research/agent-pagerank-analyzer/SKILL.md	Significantly trimmed from 306 lines to 55; new natural-language instructions are clear, but category: research uses incorrect lowercase casing, and the file is missing a trailing newline.
skills/Research/arboreto/SKILL.md	Detailed code examples replaced with concise natural-language instructions; category: research uses incorrect lowercase casing and file is missing a trailing newline.
skills/Research/biopython/SKILL.md	Well-structured Biopython skill with good module breakdown; violates the "no external URLs" checklist requirement with multiple links in the Additional Resources and Quick Reference sections.
skills/Research/audit-support/SKILL.md	Trimmed from 476 lines while keeping the manual testing checklist; still contains several external WCAG/WAI-ARIA reference URLs violating the no-external-URLs requirement.
skills/Research/agent-evaluation/SKILL.md	Original Python code-heavy skill converted to clean natural-language behavioral instructions; good structure but missing trailing newline.
skills/Research/benchling-integration/SKILL.md	Drastically trimmed from 475 lines to 34; new high-level instruction format is coherent and well-structured, though many concrete SDK examples were removed.
skills/Research/academic-researcher/SKILL.md	Frontmatter normalized — duplicate description lines removed, metadata: nesting flattened to top-level author/version fields, and examples added. Clean change.
skills/Research/bms-development/SKILL.md	Clean frontmatter update with examples added; body content is well-structured with no formatting issues.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A["PR: Update Research Skills - 20 SKILL.md files"] --> B["Frontmatter Changes"]
    A --> C["Body / Instruction Changes"]

    B --> B1["Add requires field"]
    B --> B2["Add examples field"]
    B --> B3["Normalize field order"]
    B --> B4["Flatten nested metadata to top-level"]

    C --> C1["Clean rewrites - OK\nacademic-researcher, agentdb,\nalphafold, appinsights, bms-development"]
    C --> C2["Category casing issue\nagent-pagerank-analyzer, arboreto,\nastronomy, astropy\nresearch vs Research"]
    C --> C3["Double-hash header bug\nbiorxiv-database, brenda-database,\nbioservices, box-least-squares,\ncamb-cosmology-calculator"]
    C --> C4["External URLs present\nbiopython, audit-support, ab-test-setup"]
    C --> C5["Missing trailing newline\nagent-evaluation, agent-pagerank-analyzer,\nagentdb, alphafold, arboreto,\nastronomy, astropy"]

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Comments Outside Diff (1)

1. skills/Research/biopython/SKILL.md, line 114-119 (link)

   External URLs referenced in skill instructions

   The PR checklist item "No external URLs referenced in instructions" is unchecked, and this file's "Additional Resources" section contains several external links (to the official documentation site, GitHub, tutorial pages, and the mailing list address). Skills should be self-contained and not rely on live external resources.

   The same issue exists in:

   • skills/Research/audit-support/SKILL.md (lines 101–104) which still references external WCAG and WAI-ARIA documentation URLs.
   • skills/Research/ab-test-setup/SKILL.md (line 258) which still contains a Google Analytics support link.

   These external references should be removed or replaced with inline descriptions of the relevant concepts.

_{Last reviewed commit: "fix: updated first 2..."}

[greptile-apps]

Doubled ## prefix on section headers

Multiple section headers in this file — and several other files in this PR — have been accidentally written with a double ## prefix (## ## Instruction, ## ## When to Use, ## ## Output). This will render as a literal ## Instruction heading level mismatch in Markdown and produce broken formatting.

Affected files and lines:

• skills/Research/biorxiv-database/SKILL.md: lines 12, 23, 29
• skills/Research/brenda-database/SKILL.md: lines 12, 30, 37
• skills/Research/camb-cosmology-calculator/SKILL.md: lines 12, 29, 35
• skills/Research/bioservices/SKILL.md: lines 12, 29, 36
• skills/Research/box-least-squares/SKILL.md: lines 12, 28, 34

All of these should be ## Instruction, ## When to Use, and ## Output, removing the extra ##.

Suggested change

	## ## Instruction
	## Instruction

[greptile-apps]

Inconsistent category casing

This file uses category: research (all lowercase), while the majority of skills in this repository use category: Research (title case). This inconsistency may affect category filtering or display if the system treats these as distinct values.

The same inconsistency exists in:

• skills/Research/arboreto/SKILL.md (line 5)
• skills/Research/astronomy/SKILL.md (line 6)
• skills/Research/astropy/SKILL.md (line 5)

All four should be updated to match the dominant convention.

Suggested change

	category: research
	category: Research

[greptile-apps]

Missing newline at end of file

This file (and several others in the PR) is missing a trailing newline character, as indicated by the \ No newline at end of file marker in the diff. This is a POSIX standard violation and can cause issues with some tools that process text files.

The same issue exists in:

• skills/Research/agent-evaluation/SKILL.md
• skills/Research/agent-pagerank-analyzer/SKILL.md
• skills/Research/agentdb-vector-search/SKILL.md
• skills/Research/alphafold-database/SKILL.md
• skills/Research/arboreto/SKILL.md
• skills/Research/astronomy/SKILL.md
• skills/Research/astropy/SKILL.md

Please add a trailing newline to each of these files.